Contacts of the strand formed by residues 107 - 114 (chain C) in PDB entry 3VG9
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 107 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A SER 5.3 0.6 + - - -
36A ASN* 2.8 31.0 + - - +
38A GLN 4.4 3.1 + - - -
39A ASN* 3.3 27.1 + - - +
32B SER* 5.4 5.7 - - - -
101C ASN* 4.9 8.3 - - - -
102C TYR 3.8 3.6 - - - -
103C TYR* 5.1 1.1 - - - +
106C GLY* 1.3 71.2 - - - -
108C VAL* 1.3 62.2 + - - +
109C ARG* 3.9 27.0 + - - +
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Residues in contact with VAL 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B TYR* 4.3 8.3 - - + -
50B ALA* 4.1 22.2 - - + +
100C GLY 3.4 0.7 - - - +
101C ASN* 3.2 9.8 + - - +
102C TYR* 2.7 79.5 + - + +
104C ASP* 3.1 39.3 - - + +
107C SER* 1.3 72.4 - - - +
109C ARG* 1.3 65.5 + - - +
110C TYR* 4.3 4.0 - - + -
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Residues in contact with ARG 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A ASN* 4.8 7.5 + - - -
32B SER* 6.1 2.1 - - - -
34B THR* 3.8 4.9 + - - -
49B TYR* 4.8 1.6 - - - +
50B ALA 5.2 1.7 + - - -
91B PHE* 3.0 57.1 + - + +
93B GLY 3.1 23.2 + - - +
96B TRP* 3.2 17.8 - - - -
59C ARG* 5.5 3.2 - - - +
99C GLU* 3.0 27.8 - - + +
100C GLY 3.3 6.3 - - - +
101C ASN* 3.9 13.9 + - - +
107C SER* 3.9 24.9 + - - +
108C VAL* 1.3 84.8 - - - +
110C TYR* 1.3 66.3 + - - +
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Residues in contact with TYR 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A THR* 3.2 26.2 + - - +
34B THR* 4.1 2.0 - - - +
46B LEU* 4.1 18.6 - - + -
49B TYR* 4.0 34.8 - + + -
91B PHE* 3.5 10.9 - - - -
99C GLU* 3.2 5.6 - - - +
100C GLY* 2.7 53.6 + - - -
101C ASN 4.0 7.8 + - - -
102C TYR* 3.8 31.6 - + - -
108C VAL* 4.3 2.7 - - + -
109C ARG* 1.3 84.1 - - - +
111C PHE* 1.3 64.0 + - - +
112C ASP* 3.7 30.1 - - + -
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Residues in contact with PHE 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B TYR* 3.2 32.1 + - - +
46B LEU* 3.7 6.0 - - - +
89B GLN* 3.7 18.2 - - - -
91B PHE* 3.4 23.8 - + - -
96B TRP* 3.9 4.7 - + - -
98B PHE* 4.5 0.7 - + - -
35C ASN* 3.2 48.0 - - + -
37C VAL* 4.3 11.2 - - + -
47C TRP* 4.0 11.0 - + - -
97C ALA* 3.6 20.6 - - + -
98C ARG 3.1 6.3 - - - -
99C GLU* 4.0 10.1 - - + -
110C TYR* 1.3 81.0 - - - +
112C ASP* 1.3 59.9 + - - +
113C TYR 3.5 0.9 - - - -
114C TRP* 3.1 36.4 + + - +
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Residues in contact with ASP 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B GLN* 5.9 0.9 + - - -
46B LEU* 4.1 23.0 + - + +
98C ARG* 2.9 47.3 + - - +
100C GLY* 4.2 5.1 + - - -
110C TYR* 3.7 29.9 + - + -
111C PHE* 1.3 73.9 - - - +
113C TYR* 1.3 82.9 + - + +
114C TRP* 4.4 3.9 - - - -
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Residues in contact with TYR 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217A PRO* 3.6 32.4 + - + +
219A GLU 5.3 4.2 + - - -
1C GLU 4.7 2.1 + - - -
2C VAL* 3.8 49.5 - - + +
3C GLN* 5.7 0.4 - - - -
4C LEU* 3.3 15.9 - - + +
97C ALA* 3.3 2.4 - - - -
98C ARG* 2.8 68.9 + - + -
112C ASP* 1.3 97.9 + - + +
114C TRP* 1.3 63.9 + - - +
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Residues in contact with TRP 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B TYR* 3.7 31.6 - + - -
43B SER* 4.3 7.2 - - - -
44B PRO* 3.2 58.3 + - + +
45B GLN* 4.5 10.7 + - - +
46B LEU 4.7 0.8 - - - +
98B PHE* 4.1 15.9 - + - -
4C LEU* 4.2 12.2 + - - +
37C VAL* 4.0 33.0 - - + -
45C LEU* 5.0 0.4 - - + -
95C TYR* 3.9 23.8 - + + -
96C CYS 3.6 4.0 - - - -
97C ALA* 3.9 7.6 - - + -
111C PHE* 3.1 35.0 + + + +
112C ASP 4.4 2.7 - - - -
113C TYR* 1.3 84.2 - - - +
115C GLY* 1.3 68.6 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il